VIVO as an Institutional Data Registry

The Queensland University of Technology (QUT) in Brisbane, Australia, is involved in a number of projects funded by the Australian National Data Service (ANDS). Currently, QUT is working on a project (Metadata Stores Project) that uses open source VIVO software to aid in the storage and management of metadata relating to data sets created/managed by the QUT research community. The registry (called QUT Research Data Finder) will support the sharing and reuse of research datasets, within and external to QUT. QUT uses VIVO for both the display and the editing of research metadata.

Analysis of genome survey sequences and SSR marker development for Siamese Mud Carp, Henicorhynchus siamensis, using 454 Pyrosequencing

Siamese mud carp (Henichorynchus siamensis) is a freshwater teleost of high economic importance in the Mekong River Basin. However, genetic data relevant for delineating wild stocks for management purposes currently are limited for this species. Here, we used 454 pyrosequencing to generate a partial genome survey sequence (GSS) dataset to develop simple sequence repeat (SSR) markers from H. siamensis genomic DNA. Data generated included a total of 65,954 sequence reads with average length of 264 nucleotides, of which 2.79% contain SSR motifs. Based on GSS-BLASTx results, 10.5% of contigs and 8.1% singletons possessed significant similarity (E value < 10–5) with the majority matching well to reported fish sequences. KEGG analysis identified several metabolic pathways that provide insights into specific potential roles and functions of sequences involved in molecular processes in H. siamensis. Top protein domains detected included reverse transcriptase and the top putative functional transcript identified was an ORF2-encoded protein. One thousand eight hundred and thirty seven sequences containing SSR motifs were identified, of which 422 qualified for primer design and eight polymorphic loci have been tested with average observed and expected heterozygosity estimated at 0.75 and 0.83, respectively. Regardless of their relative levels of polymorphism and heterozygosity, microsatellite loci developed here are suitable for further population genetic studies in H. siamensis and may also be applicable to other related taxa.

Corneal changes following near work in myopic anisometropia

PURPOSE: To examine the symmetry of corneal changes following near work in the fellow eyes of non-amblyopic myopic anisometropes. METHODS: Thirty-four non-amblyopic myopic anisometropes (minimum 1 D spherical equivalent anisometropia) were recruited. Corneal topography was measured with the Medmont E300 Videokeratoscope before and after a controlled near task. Subjects were positioned to minimise head movements and read continuous text on a computer monitor for 10 minutes at an angle of 25 degrees downward gaze and an accommodation demand of 2.5 D. Measures of palpebral aperture morphology during primary and downward gaze were also obtained using digital photography and analysed with customised software. RESULTS: Significant changes in corneal topography were observed after ten minutes of reading. Localised superior regions of corneal topographical change (a hyperopic shift in corneal power) were typically exhibited in both eyes following the near task. The mean change in the corneal sphero-cylinder was +0.02/-0.11 x 113 and +0.02/-0.06 x 68 for the more and less myopic eyes respectively for a 6 mm corneal diameter. A significantly greater change in corneal astigmatism power vector J0 (a larger increase in against the rule astigmatism) was observed in the more myopic eyes (p < 0.01 for a 6 mm diameter). The more and less myopic eyes exhibited a high degree of interocular symmetry for measures of palpebral aperture morphology during both primary and downward gaze. Changes in corneal power vectors following reading were associated with eyelid position during downward gaze. CONCLUSIONS: Changes in corneal topography observed following a controlled reading task were highly symmetrical between the fellow eyes of myopic anisometropes due to the interocular symmetry of the palpebral aperture. However, the more myopic eye did exhibit a small but significantly greater magnitude of change in corneal astigmatism compared to the less myopic eye following reading. These findings may have implications for understanding the mechanism of development of non-amblyopic myopic anisometropia.

Retinal and choroidal thickness in myopic anisometropia

PURPOSE: To examine the foveal retinal thickness (RT) and subfoveal choroidal thickness (ChT) between the fellow eyes of myopic anisometropes. METHODS: Twenty-two young (mean age 23 ± 5 years), healthy myopic anisometropes (≥ 1 D spherical equivalent [SEq] anisometropia) without amblyopia or strabismus were recruited. Spectral domain optical coherence tomography (SD-OCT) was used to capture images of the retina and choroid. Customised software was used to register, align and average multiple foveal OCT B-Scan images from each subject in order to enhance image quality. Two independent masked observers then manually determined the RT and ChT at the centre of the fovea from each SD-OCT image, which were then averaged. Axial length was measured using optical low coherence biometry during relaxed accommodation. RESULTS: The mean absolute SEq anisometropia was 1.74 ± 0.95 D and the mean interocular difference in axial length was 0.58 ± 0.41 mm. There was a strong correlation between SEq anisometropia and the interocular difference in axial length (r = 0.90, p < 0.001). Measures of RT and ChT were highly correlated between the two observers (r = 0.99 and 0.97 respectively) and in close agreement (mean inter-observer difference: RT 1.3 ± 2.2 µm, ChT 1.5 ± 13.7 µm). There was no significant difference in RT between the more (218 ± 18 µm) and less myopic eyes (215 ± 18 µm) (p > 0.05). However, the mean subfoveal ChT was significantly thinner in the more myopic eye (252 ± 46 µm) compared to the fellow, less myopic eye (286 ± 58 µm) (p < 0.001). There was a moderate correlation between the interocular difference in ChT and the interocular difference in axial length (r = -0.50, p < 0.01). CONCLUSIONS: Foveal RT was similar between the fellow eyes of myopic anisometropes; however, the subfoveal choroid was significantly thinner in the more myopic (longer) eye of our anisometropic cohort. The interocular difference in ChT correlated with the magnitude of axial anisometropia.

Bariatric surgery or medicine for type 2 diabetes?

Diet and medical treatment are the standard treatment for type 2 diabetes. In obese subjects with type 2 diabetes, bariatric surgery is effective in resolving diabetes. Two clinical trials comparing bariatric surgery to medical treatment were evaluated. Both the Surgical Treatment And Medications Potentially Eradicate Diabetes Efficiently (STAMPEDE) trial (laparoscopic Roux-En Y gastric bypass and sleeve gastrectomy) and the DIet and medical therapy versus BAriatric SurgerY in type 2 diabetes (DIBASY) trial (laparoscopic gastric bypass and biliopancreatic-diversion) showed that surgery was more effective than medical care in resolving or managing type 2 diabetes. Larger studies, or a compilation of studies, are needed to determine whether one of these procedures is better, or if they are all similarly effective, and this should also be weighed against the risk of the operations.

Corneal changes following near work in myopic anisometropia

Purpose: To examine the symmetry of corneal changes following near work in the fellow eyes of non-amblyopic myopic anisometropes. Methods: Thirty-four non-amblyopic, myopic anisometropes (minimum 1 D spherical equivalent anisometropia) had corneal topography measured before and after a controlled near work task. Subjects were positioned in a headrest to minimise head movements and read continuous text on a computer monitor for 10 minutes at an angle of 25 degrees downward gaze and an accommodation demand of 2.5 D. Measures of the morphology of the palpebral aperture during primary and downward gaze were also obtained. Results: The more and less myopic eyes exhibited a high degree of interocular symmetry for measures of palpebral aperture morphology during both primary and downward gaze. Following the near work task, fellow eyes also displayed a symmetrical change in superior corneal topography (hyperopic defocus) which correlated with the position of the upper eyelid during downward gaze. Greater changes in the spherical corneal power vector (M) following reading were associated with narrower palpebral aperture during downward gaze (p = 0.07 for more myopic and p = 0.03 for less myopic eyes). A significantly greater change in J0 (an increase in against the rule astigmatism) was observed in the more myopic eyes (-0.04 ± 0.04 D) compared to the less myopic eyes (-0.02 ± 0.06 D) over a 6 mm corneal diameter (p = 0.01). Conclusions: Changes in corneal topography following near work are highly symmetrical between the fellow eyes of myopic anisometropes due to the interocular symmetry of the palpebral aperture. However, the more myopic eye exhibits changes in corneal astigmatism of greater magnitude compared to the less myopic eye.

Spatial mapping of city-wide PBDE levels using an exponential decay model

Passive air samplers (PAS) consisting of polyurethane foam (PUF) disks were deployed at 6 outdoor air monitoring stations in different land use categories (commercial, industrial, residential and semi-rural) to assess the spatial distribution of polybrominated diphenyl ethers (PBDEs) in the Brisbane airshed. Air monitoring sites covered an area of 1143 km2 and PAS were allowed to accumulate PBDEs in the city's airshed over three consecutive seasons commencing in the winter of 2008. The average sum of five (∑5) PBDEs (BDEs 28, 47, 99, 100 and 209) levels were highest at the commercial and industrial sites (12.7 ± 5.2 ng PUF−1), which were relatively close to the city center and were a factor of 8 times higher than residential and semi-rural sites located in outer Brisbane. To estimate the magnitude of the urban ‘plume’ an empirical exponential decay model was used to fit PAS data vs. distance from the CBD, with the best correlation observed when the particulate bound BDE-209 was not included (∑5-209) (r2 = 0.99), rather than ∑5 (r2 = 0.84). At 95% confidence intervals the model predicts that regardless of site characterization, ∑5-209 concentrations in a PAS sample taken between 4–10 km from the city centre would be half that from a sample taken from the city centre and reach a baseline or plateau (0.6 to 1.3 ng PUF−1), approximately 30 km from the CBD. The observed exponential decay in ∑5-209 levels over distance corresponded with Brisbane's decreasing population density (persons/km2) from the city center. The residual error associated with the model increased significantly when including BDE-209 levels, primarily due to the highest level (11.4 ± 1.8 ng PUF−1) being consistently detected at the industrial site, indicating a potential primary source at this site. Active air samples collected alongside the PAS at the industrial air monitoring site (B) indicated BDE-209 dominated congener composition and was entirely associated with the particulate phase. This study demonstrates that PAS are effective tools for monitoring citywide regional differences however, interpretation of spatial trends for POPs which are predominantly associated with the particulate phase such as BDE-209, may be restricted to identifying ‘hotspots’ rather than broad spatial trends.

Queer theory, media studies and editorial processes in queer student media

Australian queer (GLBTIQ) university student activist media is an important site of self-representation. Community media is a significant site for the development of queer identity, community and a key part of queer politics. This paper reviews my research into queer student media, which is grounded in a queer theoretical perspective. Rob Cover argues that queer theoretical approaches that study media products fail to consider the material contexts that contribute to their construction. I use an ethnographic approach to examine how editors construct queer identity and community in queer student media. My research contributes to queer media scholarship by addressing the gap that Cover identifies, and to the rich scholarship on negotiations of queer community.

Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping

Prostate cancer is the most frequently diagnosed cancer in males in developed countries. To identify common prostate cancer susceptibility alleles, we genotyped 211,155 SNPs on a custom Illumina array (iCOGS) in blood DNA from 25,074 prostate cancer cases and 24,272 controls from the international PRACTICAL Consortium. Twenty-three new prostate cancer susceptibility loci were identified at genome-wide significance (P < 5 × 10−8). More than 70 prostate cancer susceptibility loci, explaining ~30% of the familial risk for this disease, have now been identified. On the basis of combined risks conferred by the new and previously known risk loci, the top 1% of the risk distribution has a 4.7-fold higher risk than the average of the population being profiled. These results will facilitate population risk stratification for clinical studies.

Fine-mapping identifies multiple prostate cancer risk loci on 5p15 some associating with TERT expression

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease.

Engaging social customers : influencing new marketing strategies for social media information sources

A global, online quantitative study among 300 consumers of digital technology products found the most reliable information sources were friends, family or word of mouth (WOM) from someone they knew, followed by expert product reviews, and product reviews written by other consumers. The most unreliable information sources were advertising or infomercials, automated recommendations based on purchasing patterns or retailers. While a very small number of consumers evaluated products online, rating of products and online discussions were more frequent activities. The most popular social media websites for reviews were Facebook, Twitter, Amazon and e-Bay, indicating the importance of WOM in social networks and online media spaces that feature product reviews as it is the most persuasive piece of information in both online and offline social networks. These results suggest that ‘social customers’ must be considered as an integral part of a marketing strategy.

Retinal and choroidal thickness in myopic anisometropia

Purpose: To compare the retinal thickness (RT) and choroidal thickness (ChT) between the fellow eyes of non-amblyopic myopic anisometropes. Methods: The eyes of 22 non-amblyopic myopic anisometropes (1 D spherical equivalent refraction [SER] anisometropia) were examined using spectral domain optical coherence tomography (SD-OCT). Customised software was used to register, align and average multiple foveal OCT B-Scan images from each subject in order to enhance image quality. Two independent masked observers manually determined the RT and ChT from each SD-OCT image up to 2.5 mm nasal and temporal to the fovea. Axial length (AXL) was measured using optical low coherence biometry during relaxed accommodation. Results: The mean SER anisometropia was 1.74 ± 0.95 D and the mean interocular AXL difference was 0.58 ± 0.41 mm. There was no significant difference in foveal RT between the fellow eyes (P > 0.05). Mean subfoveal ChT was significantly thinner in the more myopic eye (252 ± 46 μm compared to the fellow, less myopic eye (286 ± 58 μm) (P < 0.001). There was a moderate correlation between the interocular difference in subfoveal ChT and the interocular difference in AXL (r = -0.50, P < 0.01). Asian anisometropes displayed more regionally symmetrical (nasal-temporal)interocular differences in ChT profile compared to Caucasians. Conclusions: RT was similar between the fellow eyes of myopic anisometropes; however, the subfoveal choroid was significantly thinner in the more myopic (longer) eye of this anisometropic cohort. The interocular asymmetry in ChT correlated with the interocular difference in AXL.

A two-stage approach for generating topic models

Topic modeling has been widely utilized in the fields of information retrieval, text mining, text classification etc. Most existing statistical topic modeling methods such as LDA and pLSA generate a term based representation to represent a topic by selecting single words from multinomial word distribution over this topic. There are two main shortcomings: firstly, popular or common words occur very often across different topics that bring ambiguity to understand topics; secondly, single words lack coherent semantic meaning to accurately represent topics. In order to overcome these problems, in this paper, we propose a two-stage model that combines text mining and pattern mining with statistical modeling to generate more discriminative and semantic rich topic representations. Experiments show that the optimized topic representations generated by the proposed methods outperform the typical statistical topic modeling method LDA in terms of accuracy and certainty.

Mechanical properties of mussel byssus threads

The byssus threads of the common mussel, Mytilus edulis L., have been tested mechanically and the results from the tests related to the ecology of the animal. The threads are mechanically similar to other crystalline polymers such as polyethylene having a modulus of about 108N m−2 and a long relaxation time. Resilience of 60% is similar to tendon; ultimate strain is about five times that of tendon at 0.44. The thread is laid down with a prestrain of 10% and so guys the mussel in position. Calculation shows that a mussel with 50 byssus threads would be able to resist all but severe winter storms.